The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

Abstract

5Long noncoding RNAs (lncRNAs) have been shown to act as important cell biological regulators including cell fate decisions but are often ignored in human genetics. Combining differential lncRNA expression during neuronal lineage induction with copy number variation morbidity maps of a cohort of children with autism spectrum disorder/intellectual disability versus healthy controls revealed focal genomic mutations 5 0 affecting several lncRNA candidate loci. Here we find that a t(5:12) chromosomal translocation in a family manifesting neurodevelopmental symptoms disrupts specifically lnc-NR2F1. We further show that lnc-NR2F1 is an evolutionarily conserved lncRNA functionally enhances induced neuronal cell maturation and directly occupies and regulates transcription of neuronal genes including autism-associated genes. Thus, 5 5integrating human genetics and functional testing in neuronal lineage induction is a promising approach for discovering candidate lncRNAs involved in neurodevelopmental diseases. (129 words)3 Eukaryotic genomes are extensively transcribed to produce long non-coding 6 0 RNAs (lncRNAs) in a temporally and spatially regulated manner 1 . Until recently, lncRNAs were often dismissed as lacking functional relevance. However, lncRNAs are emerging as critical regulators of diverse biological processes and have been increasingly associated with a wide range of diseases, based primarily on dysregulated expression 2 .LncRNAs represent a new layer of complexity in the molecular architecture of the 6 5 genome, and strategies to validate disease relevant lncRNAs are much needed. Highthroughput analyses have shown that lncRNAs are widely expressed in the brain and may contribute to complex neurodevelopmental processes 2-9 . However, few studies have examined the role of lncRNAs in brain development mostly due to technical difficulties.Direct lineage conversion by the transcription factors Brn2, Ascl1 and Myt1l (termed 7 0 BAM factors in combination) into induced neuronal (iN) cells, recapitulates significant events controlling neurogenesis programs 10-12 , and therefore, it is a facile and informative system to study the role of lncRNAs in the establishment of neuronal identity.The noncoding genome has emerged as a major source for human diversity and disease origins. Given that less than 2% of the genome encodes protein-coding genes, the 7 5 majority of the genomic landscape is largely encompassed by non-coding elements.Efforts to identify genetic variation linked to human disease through genome-wide association studies revealed a significant majority affecting the non-coding landscape.Based on their expression and diversity in the mammalian brain, we postulate neuronal lncRNAs may be recurrently affected by mutations that disrupt normal brain function. 0Neurodevelopmental disorders manifest as a spectrum of phenotypes particularly early in life 13 . Recent studies suggest that this diversity is the result of different combinations of mutations in multiple genes, often impacting key pathways such as synap...

Invited Review: Epigenetics in neurodevelopment

“…lnc‐NR2F1 was recently identified as a candidate gene in a cohort of children with ASD/intellectual disability. lnc‐NR2F1 enhances neuronal cell maturation and regulates transcription of neuronal genes including ASD‐associated genes [179].…”

Long non‐coding NR2F1‐AS1 is associated with tumor recurrence in estrogen receptor‐positive breast cancers

“…Interestingly, the dormancy inducer DEC2, which was found equally upregulated in BT474-Var1 and BT474-Var4, activates antiapoptotic signaling in breast cancer cells, and its expression appears to be regulated by TNFa/NFjB (Li et al, 2003;Olkkonen et al, 2015). Comparative analyses for the genomic occupancy sites, by chromatin isolation by RNA purification sequencing (ChIRP-seq), suggested that NR2F1-AS1 variants can bind to distinct genomic loci acting in trans, eliciting different transcriptional responses (Ang et al, 2019). The same study revealed that NR2F1-AS1 has preference for binding DNA regions rich in basic helix loop helix (bHLH) motifs; bHLH proteins constitute a family of transcription factors implicated in circadian rhythm, cell differentiation, and hypoxia.…”

“…Thus, we wondered whether this could relate to the presence of NR2F1-AS1. regulation of neuronal fate (Ang et al, 2019). It has known 10 different variants and is located on chromosome 5q15 (Fig.…”

Interpreting the impact of noncoding structural variation in neurodevelopmental disorders

“…Very recently, differential expression analysis during mouse neuronal induction implicated the highly conserved lnc-NR2F1, transcribed divergently from the NR2F1 locus, in neurodevelopment 78 . Overlap of this lncRNA with a focal deletion found in ASD/ID patients and a newly identified, paternally inherited translocation confirmed its clinical relevance in NDD etiology (Fig.…”